DOCSLIB.ORG

Supplemental Data

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplemental Data Supplemental data Figure S1 ChIP-Seq analysis defines in vivo binding sites for Wt1 in the mouse genome (version mm10) relative to distance of transcriptional start sites. Mapping of the overlapping peaks from two independent ChIP-Seq experiments indicate that Wt1 works through both proximal and distal regulatory elements. Figure S2. Coomassie staining of SDS-PAGE gel with urine samples from inducible Wt1 podocyte-specific knock out mice. Mouse T846 with strong proteinuria served as a positive control. The first six mice showing slight proteinuria were used for the microarray experiment. 1 A B Figure S3 Neighboring motifs of Wt1 consensus sites in Wt1 up-regulated and down-regulated genes. (A) Neighboring motif of Wt1 consensus sites in Wt1 up-regulated genes indicating Sox 5 and Sox7 family binding motif. (B) Neighboring motif of Wt1 consensus sites in Wt1 down-regulated genes indicating Fox family binding motif (FoxP1, FoxP2, Foxj3, Foxj1, FoxK1 and Foxa2). 1 Figure S4. Venn diagram analysis of Wt1 up-regulated and Wt1 down-regulated genes along with podocytes enriched genes. The podocyte enriched gene list is from published data (fold change ≥ 2 compared to the rest of mouse glomeruli). 2 2 A 1.2 Nphs1 1 0.8 0.6 Nphs1 0.4 0.2 0 Control Wt1 mutant B 1.2 Sulf1 1 Sulf1 0.8 0.6 0.4 0.2 0 Control Wt1 mutant Figure S5 Wt1 positively regulates Nphs1 and Sulf1 in podocytes. (A, B) ChIP-Seq analysis on adult glomeruli identified Wt1 binding sites close to the transcription start sites of Nphs1 and Sulf1. Binding of Wt1 as viewed in the UCSC browser within the indicated genomic intervals (mm10 coordinates). ChIP product sequences on DNA are shown in red and blue for the two independent Wt1 ChIP-Seq data sets. The regions with overlaps are depicted in dark color. The peaks in the Nphs1 and Sulf1 loci are shown by a yellow line. Input control represents sequencing data of chromatin that were not subjected to immunoprecipitation. Conservation denotes placental mammal basewise conservation by Phastcons score. (C, D) Quantitative reverse transcription PCR shows the down-regulation of Nphs1 and Sulf1 after knock down of Wt1 in adult podocytes 3 Figure S6. In situ hybridization of mafbb expression in zebrafish at 48 hpf. The mafbb signal is not detectable in the glomerular region. 4 Table 1. Overview of obtained and uniquely mapped reads from two independent ChIP-Seq experiments sample Σ reads (millions) uniquely mapped reads (Bowtie1) 1st Wt1 ChIP-Seq 14.8 37% 1st Input control 21.6 42% 2nd Wt1 ChIP-Seq 57.4 37% 2nd Input control 66.8 30% Table 2 Summary of Wt1 ChIP-Seq peaks in genome indicating regulated genes. See excel file 1 Table 3 Differentially expressed gene list upon microarray analysis of wild type and mutant glomeruli. See excel file 2 Table 4. Functional annotation of microarray data by DAVID Term Count % PValue mmu04360:Axon guidance 32 1.785714 1.12E-05 mmu04142:Lysosome 30 1.674107 1.18E-05 mmu04510:Focal adhesion 41 2.287946 3.64E-05 mmu00480:Glutathione metabolism 15 0.837054 7.59E-04 mmu04810:Regulation of actin cytoskeleton 38 2.120536 0.002188 mmu04530:Tight junction 26 1.450893 0.003673 mmu00190:Oxidative phosphorylation 25 1.395089 0.004559 mmu00230:Purine metabolism 28 1.5625 0.007371 mmu00531:Glycosaminoglycan degradation 8 0.446429 0.007861 5 mmu00020:Citrate cycle (TCA cycle) 9 0.502232 0.013273 mmu04110:Cell cycle 23 1.283482 0.014815 mmu05222:Small cell lung cancer 17 0.948661 0.015628 mmu05212:Pancreatic cancer 15 0.837054 0.017522 mmu00511:Other glycan degradation 6 0.334821 0.021407 mmu00240:Pyrimidine metabolism 18 1.004464 0.022929 mmu04310:Wnt signaling pathway 25 1.395089 0.023721 mmu04340:Hedgehog signaling pathway 12 0.669643 0.024131 mmu00100:Steroid biosynthesis 6 0.334821 0.027748 mmu00520:Amino sugar and nucleotide sugar metabolism 10 0.558036 0.038478 mmu05010:Alzheimer's disease 28 1.5625 0.044132 mmu04670:Leukocyte transendothelial migration 20 1.116071 0.044433 mmu05016:Huntington's disease 28 1.5625 0.046787 mmu04120:Ubiquitin mediated proteolysis 22 1.227679 0.049049 mmu00604:Glycosphingolipid biosynthesis 5 0.279018 0.066388 mmu00970:Aminoacyl-tRNA biosynthesis 9 0.502232 0.070914 mmu04144:Endocytosis 29 1.618304 0.082863 mmu04114:Oocyte meiosis 18 1.004464 0.098234 6 Table 5 List of genes mutation of which affects podocyte structure and function in human patients.3 Those genes that were identified in this work as Wt1 targets either by ChIP-Seq or microarray are indicated. Protein Gene Associated diseases ChIP-Seq Microarray WT1 WT1 Denys-Drash syndrome (DDS) Frasier’s × syndrome (FS) Nephrin NPHS1 Congenital nephrotic syndrome of the × × Finnish type (CNF) Podocin NPHS2 Corticosteroid-resistant nephrotic × × syndrome (SRNS) PLCε1 PLCE1 Inherited nephrotic syndrome × α-Actinin-4 ACTN4 Focal segmental glomerulosclerosis × × (FSGS) INF2 INF2 FSGS × × CD2AP CD2AP Sporadic FSGS Synaptopodin SYNPO Sporadic FSGS × Myosin 1E MYO1E Childhood FSGS × LMX1B LMX1B Nail-patella syndrome × × Laminin β2 LAMB2 Pierson’s syndrome Occasionally oligosymptomatic disease TRPC6 TRPC6 FSGS MYH9 MYH9 Epstein syndrome Fechtner syndrome × × Apolipoprotein APOL1 Sporadic FSGS L-1 Glypican 5 GPC5 Acquired nephrotic syndrome 7 1. Gupta, S, Stamatoyannopoulos, JA, Bailey, TL, Noble, WS: Quantifying similarity between motifs. Genome biology, 8: R24, 2007. 2. Boerries, M, Grahammer, F, Eiselein, S, Buck, M, Meyer, C, Goedel, M, Bechtel, W, Zschiedrich, S, Pfeifer, D, Laloe, D, Arrondel, C, Goncalves, S, Kruger, M, Harvey, SJ, Busch, H, Dengjel, J, Huber, TB: Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks. Kidney international, 83: 1052-1064, 2013. 3. Greka, A, Mundel, P: Cell biology and pathology of podocytes. Annual review of physiology, 74: 299- 323, 2012. 8 Excel 1:Summary of Wt1 ChIP-Seq peaks in genome indicating regulated genes peak Chrom Start End peak score genes MACS_peak_104 chr1 73424896 73425420 166.8 Tnp1 (-409259), Tns1 (+699289) MACS_peak_107 chr1 74249326 74249802 162.28 Gpbar1 (-29036), Arpc2 (+13014) MACS_peak_109 chr1 74386418 74387312 194.52 Ctdsp1 (-4744) MACS_peak_110 chr1 75384424 75385117 133.55 Gmppa (-51172), Speg (+9474) MACS_peak_111 chr1 75387005 75387628 119.99 Gmppa (-48626), Speg (+12020) MACS_peak_113 chr1 76070680 76071302 79.87 Slc4a3 (+524725) MACS_peak_12 chr1 13372406 13373223 121.22 Prdm14 (-245652), Ncoa2 (+1268) MACS_peak_121 chr1 82291021 82291765 66.87 Irs1 (+46) MACS_peak_122 chr1 82603387 82603742 66.82 Mff (-121353), Col4a3 (+16644) MACS_peak_127 chr1 84619163 84619677 110.77 Pid1 (-334775), Dner (+76801) MACS_peak_128 chr1 85758219 85758774 236.17 Cab39 (-34950), A630001G21Rik (-21891) MACS_peak_13 chr1 13373984 13374578 72.68 Ncoa2 (-198) MACS_peak_130 chr1 86472126 86472724 71.14 Ptma (-54311), 1700019O17Rik (+46096) MACS_peak_134 chr1 88738625 88739396 83.34 Sh3bp4 (-331451), Arl4c (-36820) MACS_peak_135 chr1 88975991 88976744 99.52 Arl4c (-274177), Sh3bp4 (-94094) MACS_peak_137 chr1 89555123 89555841 185.59 Agap1 (+100671), Gbx2 (+375694) MACS_peak_138 chr1 89575672 89576063 93.36 Agap1 (+121057), Gbx2 (+355308) MACS_peak_139 chr1 89690905 89691666 78.62 Agap1 (+236475), Gbx2 (+239890) MACS_peak_14 chr1 13738208 13738825 89.58 Xkr9 (+69746), Eya1 (+571682) MACS_peak_140 chr1 90440873 90441728 189.13 Cops8 (-162124), Cxcr7 (+237298) MACS_peak_141 chr1 90442655 90443330 85.06 Cops8 (-160432), Cxcr7 (+238990) MACS_peak_142 chr1 90470732 90471552 232.8 Cops8 (-132283), Cxcr7 (+267139) MACS_peak_143 chr1 90506540 90507344 54.66 Cops8 (-96483), Cxcr7 (+302939) MACS_peak_144 chr1 91052803 91053346 107.49 Lrrfip1 (-369) MACS_peak_145 chr1 91456524 91456923 60 Hes6 (-43502), Per2 (+2604) MACS_peak_146 chr1 92687055 92687559 98.13 Gpc1 (-144379), Otos (-38466) MACS_peak_147 chr1 93176396 93176955 75.5 Sned1 (-59221), 2310007B03Rik (-15728) MACS_peak_15 chr1 13775260 13776036 93.81 Xkr9 (+106877), Eya1 (+534551) MACS_peak_16 chr1 14309840 14310749 60.45 Eya1 (-96) MACS_peak_161 chr1 106719055 106719746 71.57 Bcl2 (-5111), Kdsr (+40341) MACS_peak_162 chr1 106759460 106760044 83.05 Kdsr (-10) MACS_peak_173 chr1 119626824 119627236 100.36 Epb4.1l5 (+21970), Tmem185b (+100863) MACS_peak_174 chr1 120557132 120557827 122.87 Marco (-52396), En1 (-45007) MACS_peak_177 chr1 121327587 121328277 60.06 Insig2 (+4648), En1 (+725445) MACS_peak_178 chr1 121540398 121540864 83.79 Htr5b (-12166), Ddx18 (+27349) MACS_peak_183 chr1 125458473 125458963 171.57 Slc35f5 (-102298), Actr3 (-23228) MACS_peak_186 chr1 127306332 127306799 521.86 Mgat5 (+101580), Tmem163 (+371455) MACS_peak_188 chr1 127348552 127349233 114 Mgat5 (+143907), Tmem163 (+329128) MACS_peak_189 chr1 130455212 130455542 55.19 Daf2 (-32378), Cd55 (+7363) MACS_peak_19 chr1 19899215 19899928 287.29 Tcfap2b (+687518), Pkhd1 (+718485) MACS_peak_191 chr1 131486528 131487469 308.21 Ikbke (-207436), Srgap2 (+40362) MACS_peak_194 chr1 132335419 132335939 143.77 Nuak2 (+19554), Tmcc2 (+55602) MACS_peak_196 chr1 132417432 132417979 57.83 Dstyk (+253) MACS_peak_197 chr1 132477087 132477747 50.77 Rbbp5 (+50) MACS_peak_199 chr1 133222633 133223178 129.07 Plekha6 (-23191), Ppp1r15b (+91740) MACS_peak_200 chr1 133695993 133696556 56.74 Lax1 (-6259), Atp2b4 (+57474) MACS_peak_202 chr1 133800906 133801401 52.49 Atp2b4 (-47405), Optc (+106019) MACS_peak_206 chr1 138937686 138938298 160.3 2310009B15Rik (-81138), Dennd1b (-25717) MACS_peak_21 chr1 21052675 21053109 120.99 Tram2 (+26333), Efhc1 (+101266) MACS_peak_215 chr1 143503568 143504227 135.33 B3galt2 (-136799) MACS_peak_229 chr1 151571133 151571566
Load more

Recommended publications
  • Table 2. Functional Classification of Genes Differentially Regulated After HOXB4 Inactivation in HSC/Hpcs
    Table 2. Functional classification of genes differentially regulated after HOXB4 inactivation in HSC/HPCs Symbol Gene description Fold-change (mean ± SD) Signal transduction Adam8 A disintegrin and metalloprotease domain 8 1.91 ± 0.51 Arl4 ADP-ribosylation factor-like 4 - 1.80 ± 0.40 Dusp6 Dual specificity phosphatase 6 (Mkp3) - 2.30 ± 0.46 Ksr1 Kinase suppressor of ras 1 1.92 ± 0.42 Lyst Lysosomal trafficking regulator 1.89 ± 0.34 Mapk1ip1 Mitogen activated protein kinase 1 interacting protein 1 1.84 ± 0.22 Narf* Nuclear prelamin A recognition factor 2.12 ± 0.04 Plekha2 Pleckstrin homology domain-containing. family A. (phosphoinosite 2.15 ± 0.22 binding specific) member 2 Ptp4a2 Protein tyrosine phosphatase 4a2 - 2.04 ± 0.94 Rasa2* RAS p21 activator protein 2 - 2.80 ± 0.13 Rassf4 RAS association (RalGDS/AF-6) domain family 4 3.44 ± 2.56 Rgs18 Regulator of G-protein signaling - 1.93 ± 0.57 Rrad Ras-related associated with diabetes 1.81 ± 0.73 Sh3kbp1 SH3 domain kinase bindings protein 1 - 2.19 ± 0.53 Senp2 SUMO/sentrin specific protease 2 - 1.97 ± 0.49 Socs2 Suppressor of cytokine signaling 2 - 2.82 ± 0.85 Socs5 Suppressor of cytokine signaling 5 2.13 ± 0.08 Socs6 Suppressor of cytokine signaling 6 - 2.18 ± 0.38 Spry1 Sprouty 1 - 2.69 ± 0.19 Sos1 Son of sevenless homolog 1 (Drosophila) 2.16 ± 0.71 Ywhag 3-monooxygenase/tryptophan 5- monooxygenase activation protein. - 2.37 ± 1.42 gamma polypeptide Zfyve21 Zinc finger. FYVE domain containing 21 1.93 ± 0.57 Ligands and receptors Bambi BMP and activin membrane-bound inhibitor - 2.94 ± 0.62
    [Show full text]
  • Datasheet PB1029 Anti-AEBP2 Antibody
    Product datasheet Anti-AEBP2 Antibody Catalog Number: PB1029 BOSTER BIOLOGICAL TECHNOLOGY Special NO.1, International Enterprise Center, 2nd Guanshan Road, Wuhan, China Web: www.boster.com.cn Phone: +86 27 67845390 Fax: +86 27 67845390 Email: [email protected] Basic Information Product Name Anti-AEBP2 Antibody Gene Name AEBP2 Source Rabbit IgG Species Reactivity human,mouse,rat Tested Application WB,IHC-P,ICC/IF,FCM Contents 500ug/ml antibody with PBS ，0.02% NaN3 , 1mg BSA and 50% glycerol. Immunogen E.coli-derived human AEBP2 recombinant protein (Position: K424-Q517). Human AEBP2 shares 98.8% amino acid (aa) sequence identity with mouse AEBP2. Purification Immunogen affinity purified. Observed MW 54KD Dilution Ratios Western blot: 1:500-2000 Immunohistochemistry(Paraffin-embedded Section): 1:50-400 Immunocytochemistry/Immunofluorescence (ICC/IF): 1:50-400 Flow cytometry (FCM): 1-3μg/1x106 cells Storage 12 months from date of receipt，-20℃ as supplied.6 months 2 to 8℃ after reconstitution. Avoid repeated freezing and thawing Background Information Adipocyte Enhancer-Binding Protein is a zinc finger protein that in humans is encoded by the evolutionarily well-conserved gene AEBP2. This gene is mapped to 12p12.3. AEBP2 is a DNA-binding transcriptional repressor. It may regulate the migration and development of the neural crest cells through the PRC2-mediated epigenetic mechanism and is most likely a targeting protein for the mammalian PRC2 complex. Reference Anti-AEBP2 Antibody被引用在0文献中。 暂无引用 FOR RESEARCH USE ONLY. NOT FOR DIAGNOSTIC AND CLINICAL USE. 1 Product datasheet Anti-AEBP2 Antibody Catalog Number: PB1029 BOSTER BIOLOGICAL TECHNOLOGY Special NO.1, International Enterprise Center, 2nd Guanshan Road, Wuhan, China Web: www.boster.com.cn Phone: +86 27 67845390 Fax: +86 27 67845390 Email: [email protected] Selected Validation Data Figure 1.
    [Show full text]
  • 0.5) in Stat3∆/∆ Compared with Stat3flox/Flox
    Supplemental Table 2 Genes down-regulated (<0.5) in Stat3∆/∆ compared with Stat3flox/flox Probe ID Gene Symbol Gene Description Entrez gene ID 1460599_at Ermp1 endoplasmic reticulum metallopeptidase 1 226090 1460463_at H60c histocompatibility 60c 670558 1460431_at Gcnt1 glucosaminyl (N-acetyl) transferase 1, core 2 14537 1459979_x_at Zfp68 zinc finger protein 68 24135 1459747_at --- --- --- 1459608_at --- --- --- 1459168_at --- --- --- 1458718_at --- --- --- 1458618_at --- --- --- 1458466_at Ctsa cathepsin A 19025 1458345_s_at Colec11 collectin sub-family member 11 71693 1458046_at --- --- --- 1457769_at H60a histocompatibility 60a 15101 1457680_a_at Tmem69 transmembrane protein 69 230657 1457644_s_at Cxcl1 chemokine (C-X-C motif) ligand 1 14825 1457639_at Atp6v1h ATPase, H+ transporting, lysosomal V1 subunit H 108664 1457260_at 5730409E04Rik RIKEN cDNA 5730409E04Rik gene 230757 1457070_at --- --- --- 1456893_at --- --- --- 1456823_at Gm70 predicted gene 70 210762 1456671_at Tbrg3 transforming growth factor beta regulated gene 3 21378 1456211_at Nlrp10 NLR family, pyrin domain containing 10 244202 1455881_at Ier5l immediate early response 5-like 72500 1455576_at Rinl Ras and Rab interactor-like 320435 1455304_at Unc13c unc-13 homolog C (C. elegans) 208898 1455241_at BC037703 cDNA sequence BC037703 242125 1454866_s_at Clic6 chloride intracellular channel 6 209195 1453906_at Med13l mediator complex subunit 13-like 76199 1453522_at 6530401N04Rik RIKEN cDNA 6530401N04 gene 328092 1453354_at Gm11602 predicted gene 11602 100380944 1453234_at
    [Show full text]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Figure S1. Representative Report Generated by the Ion Torrent System Server for Each of the KCC71 Panel Analysis and Pcafusion Analysis
    Figure S1. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. A Figure S1. Continued. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. B Figure S2. Comparative analysis of the variant frequency found by the KCC71 panel and calculated from publicly available cBioPortal datasets. For each of the 71 genes in the KCC71 panel, the frequency of variants was calculated as the variant number found in the examined cases. Datasets marked with different colors and sample numbers of prostate cancer are presented in the upper right. *Significantly high in the present study. Figure S3. Seven subnetworks extracted from each of seven public prostate cancer gene networks in TCNG (Table SVI). Blue dots represent genes that include initial seed genes (parent nodes), and parent‑child and child‑grandchild genes in the network. Graphical representation of node‑to‑node associations and subnetwork structures that differed among and were unique to each of the seven subnetworks. TCNG, The Cancer Network Galaxy. Figure S4. REVIGO tree map showing the predicted biological processes of prostate cancer in the Japanese. Each rectangle represents a biological function in terms of a Gene Ontology (GO) term, with the size adjusted to represent the P‑value of the GO term in the underlying GO term database.
    [Show full text]
  • Downloaded from USCS Tables (
    bioRxiv preprint doi: https://doi.org/10.1101/318329; this version posted February 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The selection arena in early human blastocysts resolves the pluripotent inner cell mass Manvendra Singh1, Thomas J. Widmann2, Vikas Bansal7, Jose L. Cortes2, Gerald G. Schumann3, Stephanie Wunderlich4, Ulrich Martin4, Marta Garcia-Canadas2, Jose L. Garcia- Perez2,5*, Laurence D. Hurst6*#, Zsuzsanna Izsvák1* 1 Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Robert-Rössle- Strasse 10, 13125 Berlin, Germany. 2 GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain. 3 Paul-Ehrlich-Institute, Division of Medical Biotechnology, Paul-Ehrlich-Strasse 51-59, 63225 Langen, Germany. 4Center for Regenerative Medicine Hannover Medical School (MHH) Carl-Neuberg-Str.1, Building J11, D-30625 Hannover, Germany 5Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, United Kingdom 6 The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset, UK, BA2 7AY. 7 Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany. *Corresponding authors *Zsuzsanna Izsvák Max Delbrück Center for Molecular Medicine Robert Rössle Strasse 10, 13092 Berlin, Germany Telefon: +49 030-9406-3510 Fax: +49 030-9406-2547 email: [email protected] http://www.mdcberlin.de/en/research/research_teams/mobile_dna/index.html and *Laurence D.
    [Show full text]
  • Loss of the Tectorial Membrane Protein CEACAM16 Enhances Spontaneous, Stimulus-Frequency, and Transiently Evoked Otoacoustic Emissions
    The Journal of Neuroscience, July 30, 2014 • 34(31):10325–10338 • 10325 Cellular/Molecular Loss of the Tectorial Membrane Protein CEACAM16 Enhances Spontaneous, Stimulus-Frequency, and Transiently Evoked Otoacoustic Emissions Mary Ann Cheatham,1 Richard J. Goodyear,3 Kazuaki Homma,4 P. Kevin Legan,3 Julia Korchagina,3 Souvik Naskar,3 Jonathan H. Siegel,1 X Peter Dallos,1,2 Jing Zheng,4 and Guy P. Richardson3 1Roxelyn and Richard Pepper Department of Communication Sciences and Disorders, The Knowles Hearing Center, and 2Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, 3Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom, and 4Department of Otolaryngology-Head and Neck Surgery, The Knowles Hearing Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611 ␣-Tectorin (TECTA), ␤-tectorin (TECTB), and carcinoembryonic antigen-related cell adhesion molecule 16 (CEACAM) are secreted glycoproteins that are present in the tectorial membrane (TM), an extracellular structure overlying the hearing organ of the inner ear, the organ of Corti. Previous studies have shown that TECTA and TECTB are both required for formation of the striated-sheet matrix within which collagen fibrils of the TM are imbedded and that CEACAM16 interacts with TECTA. To learn more about the structural and functional significance of CEACAM16, we created a Ceacam16-null mutant mouse. In the absence of CEACAM16, TECTB levels are reduced, a clearly defined striated-sheet matrix does not develop, and Hensen’s stripe, a prominent feature in the basal two-thirds of the TM in WT mice, is absent. CEACAM16 is also shown to interact with TECTB, indicating that it may stabilize interactions between TECTA and TECTB.
    [Show full text]
  • Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected]
    University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School July 2017 Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Pathology Commons Scholar Commons Citation Mohamed, Mai, "Role of Amylase in Ovarian Cancer" (2017). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6907 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Role of Amylase in Ovarian Cancer by Mai Mohamed A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Pathology and Cell Biology Morsani College of Medicine University of South Florida Major Professor: Patricia Kruk, Ph.D. Paula C. Bickford, Ph.D. Meera Nanjundan, Ph.D. Marzenna Wiranowska, Ph.D. Lauri Wright, Ph.D. Date of Approval: June 29, 2017 Keywords: ovarian cancer, amylase, computational analyses, glycocalyx, cellular invasion Copyright © 2017, Mai Mohamed Dedication This dissertation is dedicated to my parents, Ahmed and Fatma, who have always stressed the importance of education, and, throughout my education, have been my strongest source of encouragement and support. They always believed in me and I am eternally grateful to them. I would also like to thank my brothers, Mohamed and Hussien, and my sister, Mariam. I would also like to thank my husband, Ahmed.
    [Show full text]
  • UNIVERSITY of CALIFORNIA RIVERSIDE Investigations Into The
    UNIVERSITY OF CALIFORNIA RIVERSIDE Investigations into the Role of TAF1-mediated Phosphorylation in Gene Regulation A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Cell, Molecular and Developmental Biology by Brian James Gadd December 2012 Dissertation Committee: Dr. Xuan Liu, Chairperson Dr. Frank Sauer Dr. Frances M. Sladek Copyright by Brian James Gadd 2012 The Dissertation of Brian James Gadd is approved Committee Chairperson University of California, Riverside Acknowledgments I am thankful to Dr. Liu for her patience and support over the last eight years. I am deeply indebted to my committee members, Dr. Frank Sauer and Dr. Frances Sladek for the insightful comments on my research and this dissertation. Thanks goes out to CMDB, especially Dr. Bachant, Dr. Springer and Kathy Redd for their support. Thanks to all the members of the Liu lab both past and present. A very special thanks to the members of the Sauer lab, including Silvia, Stephane, David, Matt, Stephen, Ninuo, Toby, Josh, Alice, Alex and Flora. You have made all the years here fly by and made them so enjoyable. From the Sladek lab I want to thank Eugene, John, Linh and Karthi. Special thanks go out to all the friends I’ve made over the years here. Chris, Amber, Stephane and David, thank you so much for feeding me, encouraging me and keeping me sane. Thanks to the brothers for all your encouragement and prayers. To any I haven’t mentioned by name, I promise I haven’t forgotten all you’ve done for me during my graduate years.
    [Show full text]
  • Distinct Energy Metabolism of Auditory and Vestibular Sensory Epithelia
    Distinct energy metabolism of auditory and vestibular PNAS PLUS sensory epithelia revealed by quantitative mass spectrometry using MS2 intensity Kateri J. Spinellia,b,1, John E. Klimekc,1, Phillip A. Wilmarthc, Jung-Bum Shina,b,2, Dongseok Choid, Larry L. Davidc,e, and Peter G. Gillespiea,b,3 aOregon Hearing Research Center, bVollum Institute, cProteomics Shared Resource, dDepartment of Public Health and Preventive Medicine, and eDepartment of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland OR 97239 Edited by David P. Corey, Harvard Medical School, Boston, MA, and accepted by the Editorial Board December 14, 2011 (received for review September 26, 2011) Measuring the abundance of many proteins over a broad dynamic In our experiments, we desired an accurate quantitation method range requires accurate quantitation. We show empirically that, in for relative comparisons. Because varying peptide ionization, MS2 MS experiments, relative quantitation using summed dissociation- selection, and MS2 signal render the relationship between ion-cur- product ion-current intensities is accurate, albeit variable from rent intensity and peptide abundance uncertain, we sought to em- protein to protein, and outperforms spectral counting. By apply- pirically determine the suitability of MS2 intensity for protein ing intensities to quantify proteins in two complex but related quantitation under conditions of high protein complexity. Moreover, tissues, chick auditory and vestibular sensory epithelia, we find to verify our MS2 intensity quantitation methods, we sought a direct that glycolytic enzymes are enriched threefold in auditory epithe- comparison of the molecular composition of two related but distinct lia, whereas enzymes responsible for oxidative phosphorylation biological tissues.
    [Show full text]
  • Polycomb Repressor Complex 2 Function in Breast Cancer (Review)
    INTERNATIONAL JOURNAL OF ONCOLOGY 57: 1085-1094, 2020 Polycomb repressor complex 2 function in breast cancer (Review) COURTNEY J. MARTIN and ROGER A. MOOREHEAD Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada Received July 10, 2020; Accepted September 7, 2020 DOI: 10.3892/ijo.2020.5122 Abstract. Epigenetic modifications are important contributors 1. Introduction to the regulation of genes within the chromatin. The poly- comb repressive complex 2 (PRC2) is a multi‑subunit protein Epigenetic modifications, including DNA methylation complex that is involved in silencing gene expression through and histone modifications, play an important role in gene the trimethylation of lysine 27 at histone 3 (H3K27me3). The regulation. The dysregulation of these modifications can dysregulation of this modification has been associated with result in pathogenicity, including tumorigenicity. Research tumorigenicity through the increased repression of tumour has indicated an important influence of the trimethylation suppressor genes via condensing DNA to reduce access to the modification at lysine 27 on histone H3 (H3K27me3) within transcription start site (TSS) within tumor suppressor gene chromatin. This methylation is involved in the repression promoters. In the present review, the core proteins of PRC2, as of multiple genes within the genome by condensing DNA well as key accessory proteins, will be described. In addition, to reduce access to the transcription start site (TSS) within mechanisms controlling the recruitment of the PRC2 complex gene promoter sequences (1). The recruitment of H1.2, an H1 to H3K27 will be outlined. Finally, literature identifying the histone subtype, by the H3K27me3 modification has been a role of PRC2 in breast cancer proliferation, apoptosis and suggested as a mechanism for mediating this compaction (1).
    [Show full text]
  • Ablation of Ezh2 in Neural Crest Cells Leads to Hirschsprung's Disease-Like Phenotype in Mice
    bioRxiv preprint doi: https://doi.org/10.1101/265868; this version posted February 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Ablation of Ezh2 in neural crest cells leads to Hirschsprung’s disease-like phenotype in mice Hana Kim, Ingeborg M. Langohr, Mohammad Faisal, Margaret McNulty, Caitlin Thorn, Joomyeong Kim* Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. Correspondence should be forwarded to: [email protected], 225-578-7692(ph), or 225-578-2597(fax) Running title: Function of Ezh2 in enteric neural crest cell development 1 bioRxiv preprint doi: https://doi.org/10.1101/265868; this version posted February 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract In the current study, we examined the role of Ezh2 as an epigenetic modifier for the enteric neural crest cell development through H3K27me3. Ezh2 conditional null mice were viable up to birth, but died within the first hour of life. In addition to craniofacial defects, Ezh2 conditional null mice displayed reduced number of ganglion cells in the enteric nervous system. RT-PCR and ChIP assays indicated aberrant up-regulation of Zic1, Pax3, and Sox10 and loss of H3K27me3 marks in the promoter regions of these genes in the myenteric plexus. Overall, these results suggest that Ezh2 is an important epigenetic modifier for the enteric neural crest cell development through repression of Zic1, Pax3, and Sox10.
    [Show full text]